Registering Samples

Registering Samples in Container

‚ÄčTo register samples, it is first necessary to create a new shipment, and detail information on all proteins.

  1. Ensure sample registered on UAS
  2. Create Shipment
  3. Create Protein
  4. Register Samples

Once a Shipment has been created click the "Add Container" button on a dewar in the shipment

Add Container

 

Puck / Container options

This will take you to the add container page. Here you can register samples for this puck. First select the type of container, which in most cases will be a puck:

Container type

puck dropdown

Next select the registered container from the drop-down list:
registered container drop down list
This will autopopulate the container name.

container name autopopulated

The container name is editable if needed, but it is recommended to just use the registered container name. If you need to register further containers against your proposal, please contact mx-usersupport@diamond.ac.uk for academic proposals, or industry@diamond.ac.uk for industrial proposals.

Next you should select a pipeline for priority processing:

Priority processing drop down

This defines which autoprocessing pipeline is given the highest priority. Lower priority tasks will be run on a lower priority queue, and will usually take longer to complete.

  • Available pipelines are:
    • xia2/DIALS
    • xia2/XDS
    • autoPROC.
      • autoPROC with STARANISO is run as an additional task to running autoproc.

Fast DP is prioritised above other pipelines first to give a quick result for live review of the samples. 

Show all spacegroups can be ticked if you wish to provide a space group for the sample, and thus processing pipelines, which is not normally processed for macromolecular crystallography. This may be relevant if you are looking at racemic protein crystallography or chemical crystallography. 

show all spacegroups

The spacegroups are shown under the extra-fields tab of the sample interface.

Sample Table: Basic

The interface for addding samples is split into three tabs; Basic, Extra Fields and Unattended. The minimal information for samples not for unattended data collection is the Protein Acronym and Name:

minima columns basic table

The + button, marked a below, allow you to duplicate the previous sample with a sequential name (i.e. X1 > X2). The x button, marked below, allows you to remove a sample:
buttons for interface

The samples in b are shown in the puck view c above, green filled circles implies sufficent information has been provided.

To save your new puck click "Add Container" at the bottom of the page

Add container

This will bring up a banner allowing you to see and edit the puck further in the container page.

new container bar

Sample table: Basic Fields

The protein acronym selects from a list of samples approved by Diamond Health and Safety. The samples should be submitted in advance using UAS, as the team have to review the safety information, and then a propagation from UAS to ISPyB runs. If you are unsure why a protein acronym is missing please contact mx-usersupport@diamond.ac.uk for academic proposals, or industry@diamond.ac.uk for industrial proposals.
Protein Acronym dropdown

The sample group field is currently used for VMXi and Unattended data collection (Screening).

The barcode of your pin can be provided, a check against the barcode scanned when loading the pin on the goniometer is done within GDA, and reported within ISPyB when a mismatch is found. 
barcode mismatch

The comment field is a free text field, which you can use to help organise your samples, i.e. Needle like crystal, Ethylene glycol dip soak at 25%.

Automated Phasing Pipelines

To run automated phasing pipelines (Fast EP or Big EP)  the anomalous scatterer must be supplied in the sample registration. 

anomalous scatterer dropdown

 

Sample Table: Extra Fields

The extra fields tab contains a few optional fields:

Extra Fields

The user path adds an extra folder structure to file path

i.e /dls/i03/data/2021/<visit>/auto/userpath1/userpath2/<protein_acronym>/<sample_name>/

The spacegroup can be provided to trigger autoprocessing assuming that space group, which may be useful to give results in the expected space group, especially when it may be hard to determine automatically. We will also run autoprocessing without knowledge of the space group.

Sample Table: Unattended

Details on unattended collection are given in Preparation for UDC.

Cloning Samples in the Puck

Samples can be cloned from the first line of the table using the Clone from first sample button:

Clone from first

This will populate all spaces in the puck:

cloned all

Lines can be deleted or altered to add different samples to a puck.

Error reporting

Errors are reported if the container cannot be submitted:, in a red text box above the Add container button. These diappear live as the error is fixed.
Error reporting

Uploading via a CSV file

See Uploading samples using CSV file for uploading a larger number of samples. 

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